The former England captain was cleared of racially abusing Ferdinand at a London court hearing on July 13.
However, the FA said in a statement they had now charged Terry after reviewing evidence gathered in their own inquiry in addition to the criminal investigation.
Terry was found not guilty after a five-day trial at Westminster Magistrates Court which delved into the circumstances surrounding an incident involving the two players during a Premier League match on October 23 last year.
In a statement, the FA said: "After seeking advice from an external Independent QC, and having considered the evidence and Magistrates' Court decision in the John Terry case, The FA has today charged the Chelsea player following an alleged incident that occurred during the Queens Park Rangers versus Chelsea fixture at Loftus Road on 23 October 2011.
"It is alleged that Terry used abusive and/or insulting words and/or behaviour towards Queens Park Rangers' Anton Ferdinand, contrary to FA rules.
"It is further alleged that this included a reference to the ethnic origin and/or colour and/or race of Anton Ferdinand," the FA said in a statement released just hours before Friday's opening ceremony of the London Olympic Games.
"This charge is the result of The FA's long-standing enquiries into this matter, which were placed on hold pending the outcome of the criminal trial, and relates to rules governing football only," the statement went on.
The FA added that Terry remains available to play for England and has until 3 August 2012 to respond to the charges.
"The FA will make no further comment during this time," the statement concluded.
Terry was stripped of the England captaincy in February over the allegations. As a consequence, Fabio Capello resigned as England manager, just months before Terry joined the England squad for the 2012 European Championships.
Meanwhile, the FA put their own disciplinary process on hold so as not to prejudice the trial.
But following the outcome English football's governing body reacted to the court verdict by saying it noted the decision but would still proceed with and conclude its own enquiries which require a lower standard of proof than in a criminal trial.
Lord Herman Ouseley, chairman of the Kick it Out campaign which seeks to eradicate racism from football, had following the court verdict urged the FA to take its own, independent, action.
"There is only one regulatory body for football and it's not the courts," Ouseley told Sky Sports.
He added: "The Football Association would have already concluded its investigations and its processes had the courts not intervened through the police and the Crown Prosecution Service.
"Their prosecution and evidence was inadequate and John Terry has been cleared of what he was charged on."
Asked if the verdict could deter players who had been racially abused coming forward in future, Ouseley said: "There is clear evidence we know that players are reluctant to come forward and raise this issue.
Source: AFP
Source: AFP